Site-Specific Stabilization of DNA by a Tethered Major Groove Amine

Oct 16, 2013 - ... temperature revealed that the X5 imino resonance remained sharp at 55 °C. Additionally, two 5′-neighboring base pairs, A4:T9 and...
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Site-Specific Stabilization of DNA by a Tethered Major Groove Amine, 7‑Aminomethyl-7-deaza-2′-deoxyguanosine Marta W. Szulik,† Markus W. Voehler,† Manjori Ganguly,‡ Barry Gold,‡ and Michael P. Stone*,† †

Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States

‡

S Supporting Information *

ABSTRACT: A cationic 7-aminomethyl-7-deaza-2′-deoxyguanosine (7amG) was incorporated site-specifically into the selfcomplementary duplex d(G1A2G3A4X5C6G7C8T9C10T11C12)2 (X = 7amG). This construct placed two positively charged amines adjacent to the major groove edges of two symmetryrelated guanines, providing a model for probing how cation binding in the major groove modulates the structure and stability of DNA. Molecular dynamics calculations restrained by nuclear magnetic resonance (NMR) data revealed that the tethered cationic amines were in plane with the modified base pairs. The tethered amines did not form salt bridges to the phosphodiester backbone. There was also no indication of the amines being capable of hydrogen bonding to flanking DNA bases. NMR spectroscopy as a function of temperature revealed that the X5 imino resonance remained sharp at 55 °C. Additionally, two 5′-neighboring base pairs, A4:T9 and G3:C10, were stabilized with respect to the exchange of their imino protons with solvent. The equilibrium constant for base pair opening at the A4:T9 base pair determined by magnetization transfer from water in the absence and presence of added ammonia base catalyst decreased for the modified duplex compared to that of the A4:T9 base pair in the unmodified duplex, which confirmed that the overall fraction of the A4:T9 base pair in the open state of the modified duplex decreased. This was also observed for the G3:C10 base pair, where αKop for the G3:C10 base pair in the modified duplex was 3.0 × 106 versus 4.1 × 106 for the same base pair in the unmodified duplex. In contrast, equilibrium constants for base pair opening at the X5:C8 and C6:G7 base pairs did not change at 15 °C. These results argue against the notion that electrostatic interactions with DNA are entirely entropic and suggest that major groove cations can stabilize DNA via enthalpic contributions to the free energy of duplex formation. DNA.16 A 7-hydroxymethyl-7-deazaguanine (7hmG) isostere was shown to be as destabilizing as (or more destabilizing than) the c7G nucleotide, indicating the critical role of the cationic charge in the enthalpic stabilization.16 This effect was in contrast to salt bridge formation involving the phosphate backbone that is considered to be entropy-driven.17 Molecular modeling suggested that the tethered cation introduced by 7amG was located in the major groove and did not form a salt bridge with the flanking bases or backbone. In this study, this important structural feature of the model is confirmed and the local stabilization of base pairing at and flanking the 7amG nucleotide in the 5′-direction is demonstrated. This structural information supports the contention that major groove cations that do not make any electrostatic contact with the DNA can stabilize the duplex because of an enthalpic effect, which may also be used by proteins in their recognition of specific DNA sequences.

DNA is a polyanion that is effectively neutralized with diffusible cations even at low salt concentrations.1−3 The formation of electrostatic salt bridges between the nonbridging phosphate oxygens and basic amino acids of DNA binding proteins releases cations to the bulk solvent, providing a non-sequencespecific entropic driving force for protein−DNA binding.4,5 In high-resolution crystallography, mono- and divalent cations are often observed at the major groove edge of guanines.6−11 Positively charged basic amino acid side chains are often observed at the same locations.12 The presence of diffusible and protein-tethered cations suggests that they stabilize the ensemble of nucleic acid, water, and salt. We reported that disruption of such major groove cation binding sites by the substitution of 7-deazaG (c7G)13 or 8-oxoguanine (8oG)14 was destabilizing because of a reduction in the enthalpy term that was not fully compensated by an increase in entropy. To further explore the thermodynamic role of major groove cations in DNA stability, we created a model system to recapitulate the observed locations of major groove monovalent cations by synthesizing 7-aminomethyl-7-deazaguanine (7amG)15 and incorporating it into sites with different flanking sequences.16 The covalent tethering of a cation in the major groove at c7G restored the stability of the DNA to that of the unmodified © 2013 American Chemical Society

Received: June 1, 2013 Revised: September 5, 2013 Published: October 16, 2013 7659

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MATERIALS AND METHODS The unmodified oligodeoxynucleotides were synthesized by the Midland Certified Reagent Co. (Midland, TX) and purified by anion exchange high-performance liquid chromatography (HPLC). The phosphoramidite derivative of 7-aminomethyl7-deaza-dG (7amG) nucleoside was synthesized as described previously15 and incorporated into 5′-d(GAGAXCGCTCTC)3′, where X represents 7amG. The purities of the oligodeoxynucleotides were verified by HPLC using a semipreparative reverse-phase column (YMC, C18, 5 μm, 250 mm × 10.0 mm) equilibrated with 0.1 M ammonium formate (pH 7.0). All of the oligodeoxynucleotides were desalted using G-25 Sephadex, lyophilized, and characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (calculated mass for [M − H]− m/z 3674.5, found m/z 3674.8). The oligodeoxynucleotides were annealed in appropriate buffers, being heated to 85 °C for 15 min and and cooled to room temperature. The oligodeoxynucleotide concentrations were determined by UV absorbance at 25 °C using an extinction coefficient of 1.11 × 105 M−1 cm−1 at 260 nm.18 NMR. The modified and unmodified samples were dissolved to a duplex concentration of 0.25 mM in 180 μL of 200 mM NaCl, 50 μM Na2EDTA, and 10 mM NaH2PO4 (pH 7.0). The samples were exchanged with D2O and dissolved in 180 μL of 99.99% D2O to observe nonexchangeable protons in the spectra. For the observation of exchangeable protons, the samples were dissolved in 180 μL of a 9:1 H2O/D2O mixture. The NOESY and DQF-COSY spectra of samples in D2O were collected at 25 °C on a Bruker AV-III 800 MHz spectrometer using a CPTCI probe. For the assignment of exchangeable protons, NOESY experiments with mixing times of 150, 200, and 250 ms and TPPI quadrature detection were conducted. These data were recorded with 2048 real data points in the t2 dimension and 1024 data points in the t1 dimension. The relaxation delay was 2.0 s. The data in the t1 and t2 dimension were zero-filled to give a matrix of 2K × 2K real points. The NMR spectra for the exchangeable protons were recorded at 5, 15, 25, 35, 45, 55, and 65 °C on a Bruker AV-III 600 MHz spectrometer equipped with a CPQCI probe. The NOESY19,20 spectra of unmodified and modified samples in H2O were collected at 5 °C with mixing times of 70 and 250 ms at 600 MHz. Water suppression was achieved by a gradient Watergate pulse sequence.21 Chemical shifts were referenced to water. NMR data were processed with TOPSPIN version 2.0.b.6 (Bruker Biospin Inc., Billerica, MA). Experimental Distance Restraints. The volumes of crosspeaks for the NOESY spectrum recorded at a mixing time of 250 ms were obtained using SPARKY.22 These were combined with intensities generated from the complete relaxation matrix analysis of a starting structure23 to generate a hybrid intensity matrix. To refine the hybrid intensity matrix and optimize the agreement between calculated and experimental NOE intensities, MARDIGRAS24 was used. The RANDMARDI25 algorithm conducted 50 iterations for each set of data, randomizing peak volumes within limits specified by the input noise level. The molecular motion was assumed to be isotropic. The volume error was defined as one-half the volume of the weakest cross-peak. Calculations were performed using a B-DNA initial structure26 generated using INSIGHT II (Accelyris, Inc., San Diego, CA), and NOE intensities derived from experiments with a mixing time of 250 ms, and with three isotropic correlation times (2, 3, and 4 ns), yielding three sets

of distances. Analysis of these data yielded the experimental distance restraints and standard deviations for the distance restraints used in subsequent restrained molecular dynamics calculations. For partially overlapped cross-peaks, the upper bounds on the distances were increased. Additional empirical restraints for base pair, phosphodiester backbone, and deoxyribose pseudorotation were obtained from canonical values derived from B-type DNA.26 Restrained Molecular Dynamics (rMD) Calculations. Classical B-DNA26 was used as the reference to create the starting structure for rMD calculations. The 7amG adduct was constructed by bonding the aminomethyl group to the C7 atom on the G5 nucleotide in both strands, using INSIGHT II. The coordinates, connectivity, and parameters for the models were obtained from xLEaP.27 The restrained electrostatic potential charges for the 7amG adduct were calculated with the B3LYP/ 6-31G* basis set using GAUSSIAN.28 The starting structure was energy minimized for all atoms using AMBER.29 The rMD calculations were performed with AMBER29 using a simulated annealing protocol with the parm99 force field.30 Calculations performed in vacuo were initiated by coupling to a heating bath with a target temperature of 600 K. The generalized Born method was used to model solvation.31,32 The force constants for empirical hydrogen bonding and all NOE restraints were maintained at 32 kcal mol−1 Å−2. Initially, 20000 steps of a simulated annealing protocol were performed. The system was heated from 0 to 600 K for the first 1000 steps, with a coupling of 0.5 ps. During steps 1001−2000, the system was maintained at 600 K and then cooled to 100 K over 18000 steps with a coupling of 4 ps. The final cooling from 100 to 0 K during steps 18001−20000 was performed with a coupling of 1 ps. Subsequently, a 100000-step simulated annealing protocol with an integrator time step of 1 fs was performed. The system was heated to 600 K in 5000 steps, maintained at 600 K for 5000 steps, and then cooled to 100 K with a time constant of 4.0 ps over 80000 steps. A final cooling stage was applied to relax the system to 0 K with a time constant of 1.0 ps over 10000 steps. After each cycle, a set of structural coordinates was saved for energy minimization. To obtain an average structure, 10 emergent structures were chosen on the basis of the lowest deviations from the experimental distance and dihedral restraints and were energy minimized. Back-calculations of theoretical NMR intensities from the emergent structure were performed using CORMA.33 Measurement of Base Pair Opening. NMR data were collected at 15 °C at 500 MHz using a Bruker AV-III spectrometer equipped with a 5 mm CPQCI probe. The samples were dissolved in 180 mL of a 90% H2O/10% D2O solution containing 100 mM NaCl, 0.05 mM Na2EDTA, 0.011 M NaN3, 1 mM triethanolamine, and 10 mM NaH2PO4 (pH 8.0). The transfer of magnetization from water to the imino protons was followed by observation of the imino protons after a variable mixing time.34 For selective spin inversion of the water protons, a 2 ms 180° sinc pulse with 1000 points was used. To minimize effects of radiation damping during the mixing time, a 0.1 G/cm gradient was used. Water suppression was achieved by a binominal 1−1 echo sequence, jump and return,35 with flanking 1 ms smooth square shape gradients, 15 G/cm. Sixteen values of the variable delay ranging form 1 ms to 15 s were used for each experiment. All data were processed and analyzed with TOPSPIN. Ammonia was used as the acceptor because of its small size and lack of charge and to minimize catalysis due to the presence of OH− ions.34 The 7660

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ammonia-catalyzed exchange was measured at pH 8.36−40 The ammonia was titrated from stock solutions, with concentrations that ranged from 0.1 to 5 M. The DNA samples contained 1 mM triethanolamine, which was used to monitor the pH of the NMR sample during the titration, in situ, by measuring the chemical shift difference between the two methylene groups.36 The pKa of 9.22 for ammonia at 15 °C was used. The concentration of the ammonia base was calculated from the total ammonia concentration (c0) and the pH as [B] = c0

10−pK 10−pH + 10−pK

Scheme 1. (A) Structure of the X = 7-Aminomethyl-7-deazadG (7amG) Modificationa and (B) Sequences and Numbering of the Nucleotides for Unmodified OL-1a and Modified OL-1b Duplexes

(1)

The data analysis and fits were performed using PRISM version 6.0b (GraphPad Software, Inc., La Jolla, CA). The exchange rates in the absence and presence of added ammonia were calculated from the equation Iz(tmix ) = 1 + Ekex(e−R1itmix − e−R1wtmix ) Iz,eq

(2)

where Iz(tmix) and Iz,eq are intensities of the imino proton peaks at a given value of tmix and at equilibrium, respectively, kex is the chemical exchange rate, R1w is the longitudinal relaxation rate of water, 3.15 s as determined separately under the same conditions, R1i is the sum of the imino proton relaxation rate and kex, and E is the efficiency of water inversion using the value of −2.41,42 In general, equilibrium constants for base pair opening were calculated by fitting the imino exchange rate data as a function of ammonia concentration to the equation36 kex = KopkB[B] =

kop kcl

kB[B]

a

The 7-aminomethyl moiety is colored red.

protons and the deoxyribose H1′ protons were of the same relative magnitudes as those between other bases in the sequence. The 7amG H8 resonance was observed at 6.4 ppm, shifted upfield by approximately 1 ppm with respect to that of the unmodified oligodeoxynucleotide. This was attributed to the differential electronic density for c7G as compared to G. Proton resonances from the neighboring A4 and C6 bases exhibited chemical shift changes of 5 Å away. Moreover, the cationic amine is not located within H-bonding distance of the flanking base pairs. If H-bonding were an important factor in the stabilization, then this would have been observed for the hydroxymethyl analogue. This was not the case.16 There is also no evidence of a change in major groove dimension because of the collapse of the phosphate backbone onto the tethered cation, as has been predicted for divalent cations as a source of DNA bending.17 The NMR data indicate that the site-specific positioning of this cationic amine does not greatly alter the structure of the OL-1b duplex, as compared to the unmodified OL-1a duplex. This suggests that the enthalpic stabilization of the OL-1b duplex by the 7amG modification16 is not due to intrinsic differences in either base stacking or Watson−Crick hydrogen bonding (Figure 7). Figure 1 reveals only minor chemical shift changes for the base aromatic and deoxyribose H1′ protons of the two duplexes. A comparison of the chemical shifts of the Watson−Crick imino base-paired protons and amino basepaired protons (Figure 3) also shows minimal differences between the OL-1a and OL-1b duplexes, consistent with the conclusion that the site-specific positioning of the tethered amine in the major groove has a negligible effect upon the structure of this duplex in solution. Site-Specific Positioning of Cations in the DNA Major Groove. Studies of the regioselectivity of DNA alkylation at the N7-dG position by a series of alkylating agents have revealed that compounds reacting with DNA via methanediazonium ion (CH3N2+) intermediates, such as methylnitrosourea (MNU),52 produce sequence-dependent alkylation patterns.53−55 Similar patterns have been observed for nitrogen mustards,56 N-nitrosoureas,57,58 and triazenes.59 These effects are muted if the alkylation is conducted in ssDNA versus dsDNA.60 Collectively, these data suggest that at the microscopic level, the electrostatic landscape of DNA exhibits major groove sequence specificity,61 in addition to the counterion condensation theory of overall DNA charge neutralization,1−3 which is not predicted to exhibit sequence specificity. Braunlin and co-workers6,62,63 have shown that di- and trivalent ions, including Mg2+, Ca2+, and Co3+, preferentially associate with the major groove of DNA at dG:dC base pairs, and they have proposed that neighboring dG’s provide sequence-specific divalent cation binding sites because they can exploit the spatial relationship between the N7 and O6 atoms of the dG base.6 High-resolution crystallographic experiments often allow the observation of specific cations in the major groove near dG:dC base pairs and in the minor groove near dA:dT base pairs.11 The self-complementary DDD has been crystallized in the presence of Tl+, providing the

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SUMMARY The consequences of site-specifically placing a cationic 7aminomethyl-7-deaza-2′-deoxyguanosine (7amG) into d(GAGAXCGCTCTC)2, where X = 7amG, have been explored. The tethered cationic amines are in plane with the modified base pairs. The X5:C8 base pair is stabilized. Additionally, the two 5′neighboring A4:T9 and G3:C10 base pairs are stabilized with respect to the exchange of their imino protons with water. The equilibrium constant for base pair opening decreases for base pair A4:T9 as compared to that for base pair A4:T9 in the unmodified duplex, indicating that the overall fraction of base pair A4:T9 in the open state of the modified duplex decreases. A smaller decrease in the equilibrium constant for base pair opening is observed for base pair G3:C10. The fact that the enthalpic stabilization of the modified OL-1b duplex16 not only involves the modified X5:C8 base pair but also extends in the 5′direction to involve the A4:T9 and G3:C8 base pairs provides a new example of cation-mediated sequence-specific modulation of DNA stability.

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ASSOCIATED CONTENT

S Supporting Information *

1

H chemical shifts of the nonexchangeable protons of the OL1b duplex (Table S1), NOE distance restraints used for the structural refinement of the OL-1b duplex (Table S2), backbone restraints generated for the OL-1b duplex used in rMD calculations (Table S3), deoxyribose restraints generated for the OL-1b duplex used in rMD calculations (Table S4), base pair restraints generated for the OL-1b duplex used in rMD calculations (Table S5), base pairing and base stacking helicoidal parameters of the refined structure of the OL-1b duplex (Table S6), backbone torsion angles of the refined OL1b duplex with averaged values from two symmetry-related strands (Table S7), backbone torsion angles of the refined OL1b duplex (Figure S1), line widths of the guanine N1H and thymine N3H imino proton resonances as a function of temperature (Figure S2), and representative time courses of transfer of solvent magnetization to the imino protons for the OL-1a and OL-1b duplexes (Figure S3). This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Telephone: (615) 322-2589. 7666

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Funding

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This work was supported by National Institutes of Health (NIH) Grants P01 CA-160032 and R01 ES-05509 (M.P.S.), R01 CA-76049 (B.G.), and R01 CA-29088 (B.G.). Additional support for core instrumentation was provided by NIH center grants P30 ES-00267, Vanderbilt University Center in Molecular Toxicology, and P30 CA-068485, Vanderbilt-Ingram Cancer Center. Funding for NMR was supplied by NIH Grants S10 RR-05805 and S10 RR-025677 and National Science Foundation Grant DBI 0922862, the latter funded by the American Recovery and Reinvestment Act of 2009 (Public Law 111-5), and by Vanderbilt University. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We thank Prof. Carmelo J. Rizzo and Ms. Albena Kozekova for assistance with the synthesis of the 7amG-modified oligodeoxynucleotide.

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dx.doi.org/10.1021/bi400695r | Biochemistry 2013, 52, 7659−7668